#!/usr/bin/python
from __future__ import division
from __future__ import with_statement
import os
import sys
import toolbox_idynomics
import toolbox_plotting
path = sys.argv[1]
sim_dir = toolbox_idynomics.SimulationDirectory(path)
color_dict_path = os.path.join(sim_dir.figures_dir, 'color_info.txt')
if os.path.isfile(color_dict_path):
species_color_dict = toolbox_idynomics.read_color_dict(color_dict_path)
else:
species_color_dict = toolbox_idynomics.get_default_species_colors(sim_dir)
toolbox_idynomics.save_color_dict(species_color_dict, color_dict_path)
fig = toolbox_plotting.PlosFigure()
axis = fig.add_subplot('', 111)
plot_left, plot_right, text_left = 30, 35, 38
y, y_diff = 100, -60
max_time = 1
max_abundance = 1
for species_name in sim_dir.get_species_names():
time = []
abundance = []
for iter_info in sim_dir.get_iterate_information():
sim = toolbox_idynomics.SimulationDirectory(options.results_dir)
if not options.file_ext[0] == '.':
options.file_ext = '.'+options.file_ext
save_name = 'biofilm_'+options.solute_name
num_digits = len(str(sim.get_last_iterate_number()))
color_dict_path = os.path.join(sim.figures_dir, 'color_info.txt')
if os.path.isfile(color_dict_path):
species_color_dict = toolbox_idynomics.read_color_dict(color_dict_path)
else:
species_color_dict = toolbox_idynomics.get_default_species_colors(sim)
toolbox_idynomics.save_color_dict(species_color_dict, color_dict_path)
nI, nJ, nK, res = sim.find_domain_dimensions()
if options.i_max > 0:
nI = options.i_max
counter = 0
if options.figure_type == None:
if options.height > 0: height = options.height
else: height = toolbox_plotting.mm2inch(nI * res)
if options.width > 0: width = options.width
else: width = toolbox_plotting.mm2inch(nJ * res)
figure = toolbox_plotting.SlideFigure(width=width, height=height)
else:
def isPredecessor(early, late):
if not ( early.vars['family'] == late.vars['family'] ):
return False
early_genealogy = int(early.vars['genealogy'])
late_genealogy = int(late.vars['genealogy'])
late_generation = int(late.vars['generation'])
return (late_genealogy == early_genealogy + 2**(late_generation))
for path in args:
sim_dir = toolbox_idynomics.SimulationDirectory(path)
color_dict_path = os.path.join(sim_dir.figures_dir, 'color_info.txt')
if os.path.isfile(color_dict_path):
species_color_dict= toolbox_idynomics.read_color_dict(color_dict_path)
else:
species_color_dict = \
toolbox_idynomics.get_default_species_colors(sim_dir)
toolbox_idynomics.save_color_dict(species_color_dict, color_dict_path)
fig = toolbox_plotting.PlosFigure()
axis = fig.add_subplot('', 111)
max_time = 0.0
max_val = 0.0
min_val = 0.0
cells = []
for iter_info in sim_dir.get_iterate_information():
max_time = max(max_time, iter_info.time)
for cell in iter_info.agent_output.get_all_cells():
family = int(cell.vars['family'])
genealogy = int(cell.vars['genealogy'])
attribute_val = float(cell.vars[options.attribute])
max_val = max(max_val, attribute_val)
min_val = min(min_val, attribute_val)